The Caged Bird Hypothesis
by Princess-Warrior 17
Summary: "This isn't easy to say because I love you, but I need some time to take a step back and reevaluate our situation. I hope you understand." As much as it pained Amy to say those words to Sheldon, she knew she had to. Ever since then, she has struggled with what she wants and who she is. Join her as she embarks on a journey of self-discovery and healing. Post 8x24.
1. The Sweetest Sorrow

**A/N:**

 _As stated in the summary, this story is based on the events of the Season 8 finale. Some of you can probably guess that watching it kind of killed me on the inside. Despite the fact that it left me with a roller coaster of emotions, I definitely have hope for Sheldon and Amy for Season 9. Until then, this fan-fic is my source of therapy. It's my greatest hope that it serves as a form of therapy for all of the Shamy shippers out there, too._

 _There's a lot to be said about the finale, but I won't waste your time with my opinions. I'll let my writing do the talking. This story is going to span across the hiatus, so please don't expect weekly updates. In addition, this is my first time writing for The Big Bang Theory fandom, so I apologize if it's not up to par with some of the other writers. I'm not fluent in Sheldon or Amy speak, so there may be times where they seem out of character. Just a warning. I tried, but I'm nowhere near as brilliant as the writers for the show are._

 _One more note: the story will mostly capture Amy's perspective. Upon occasion, we will get a look at what's going on in Dr. Cooper's head._

 _Without further ado…_

 **Disclaimer:**

 _I do not own The Big Bang Theory. Chuck Lorre, Bill Prady, and CBS do._

* * *

 **The Caged Bird Hypothesis**

Chapter 1: The Sweetest Sorrow

"There ain't no way you can hold onto something that wants to go, you understand? You can only love what you got while you got it."

–Kate DiCamillo, _Because of Winn-Dixie_

* * *

 **May 21, 2015**

It had been two weeks. Two _very long_ weeks.

Sheldon didn't want to admit it, but every single minute that ticked by when he didn't hear from Amy made his stress levels rise. His nerves felt like they were hot-wired; a feeling that was comparable to the period in his life when he tried to purposefully induce anxiety in order to increase his productivity. As if that wasn't bad enough, this was much worse _._

Recently, he found that his heart raced slightly faster than its normal perfect rhythm and that despite the copious amounts of Advil he ingested, the constant throbbing pain near his temples would not cease. There was even a tiny tremor in his hands when one looked hard enough. His shoulders remained stiff, no matter how much he attempted to relax them. His natural, lopsided grin, which he had allowed himself to show more in the last six months, started to dissolve into the tight-lipped mold he had perfected for occasions when he was forced to smile. And if one looked even harder, _really_ looked, one could see that his blue eyes hadn't lit up in happiness or amusement in the last couple of weeks.

He feigned enthusiasm as best as he could, but he knew acting wasn't his forte. A shame, really, since everything else was.

Even though the inside of Sheldon's mind (and heart) was consumed with confusion and sorrow, he kept a detached demeanor on the outside, making sure to appear as if he wasn't affected by Amy's absence. He knew his mistake with Zazzles and the other cats. It was obvious (even to him, after much introspection) that he had acted upon his feelings of loneliness. Years had passed since that incident, and now, he believed that he could appear nonchalant about the situation without purchasing twenty-five pets (or other unnecessary items to fill the void). And that's exactly what he was doing.

He continued on his progress with Dark Matter, filling white board after white board with more equations and theories. He chatted animatedly about the newest editions available at the comic book store, re-watched _Star Wars_ and _Star Trek_ with his friends, and played Halo and paintball with a gusto he hadn't experienced for the last couple of years. He still scoffed at anything Wolowitz said, rolled his eyes at the bantering between Leonard and Penny (both of whom had returned from Las Vegas declaring that they thought a last minute wedding wasn't their style because it didn't include the people most important to them), and often reminded Raj that staying with Emily was a horrid idea because he still had to work on issues with being alone.

All in all, it seemed that Sheldon had everything under control. His years of indifference and apathy had served him well. He was an emotionless wall who could blink and blurt out anything that came to mind, regardless of the appropriate social protocol. It was true that he didn't quite understand the pleasure of having emotions. After all, he was above emotions—they were petty things that were waste of time. Biologically speaking, yes, he did have a heart. But, it pumped blood, and other than keeping him alive, that organ had no business interfering with what one would call _'love_. _'_

That was so far from the truth that it was funny.

Years ago, he was delighted because everyone—colleagues, friends, and family-thought he was an emotionless wall. He _didn't care_ back then. The only thing that mattered was his ability to express his genius. The world deserved to know how brilliant he was. The world _needed_ to know how much they should appreciate Sheldon Lee Cooper. Then again, he knew how some people could resist this idea. It was silly to him, of course, but he was aware that 'haters' existed. Every harsh comment thrown his way, every annoyed glance was ignored. Plebeians could be ignored. What couldn't be, though, was that Sheldon Cooper was the best Homo Novus, and _nothing_ could alter that fact.

But, ever since he had laid eyes on all five feet, four inches of Amy Farrah Fowler, with her sharp tongue that could refute any point of his, and clad in her purple and black striped cardigan, khaki colored skirt, orthopedics, and thinly framed glasses, things had been different.

Through the five years they had spent together, including the many arguments, intelligent conversations, Date Nights, and evenings of drinking tea and enjoying the comfortable silence that they shared from time to time, the wall that he had spent years constructing had begun to crack, a little bit at a time. It had never crumbled completely, and for that, he was grateful. Even though she had changed him, there were parts of his personality—his quirks, as he liked to call them—that could never alter or disappear altogether.

When he took the time to really think about how much he had emotionally and mentally grown _because_ of her, it terrified him. It meant that she had a greater influence in his life than he'd care to admit.

And that was why the bravado he kept up took a tremendous amount of effort. Sure, he didn't have a lot of difficulty finding things to ponder—particle physics, superheroes, the movies that he had seen and the many that he still wanted to see, a multitude of video games, the perfect nature of his spot on the couch, his interesting relationships with his friends, how his mother was fairing in East Texas, the list kept going on and on. The difficult part was forcing himself to focus on these other subjects and not _her._

What frightened him more than anything was that he thought about her a little too much. Whenever he saw the color green, he was reminded of her sparkling eyes that always managed to make his lips quirk into a small smile. Whenever someone would laugh, he immediately thought about the times his ears had picked up on her quiet chuckle. She had a musical lilt that he liked. There was something _endearing_ about it, something that he couldn't quite understand, but like many aspects of life he found puzzling, he just learned to accept it.

What hurt the most, though, was when everyone else had their respective partner beside them, either at dinner in 4A, or out and about. He tried to ignore the small looks of affection passing between couples, or the hand holding, or the occasional kiss. He would have to look away in those moments, for sake of their privacy, and because it was simply proof that he had no one to share those things with now. The emptiness that was there made him think about the years before he met Amy. And despite his efforts to deny it, he didn't want to go back to that time of his life. Loneliness had been his companion for far too long. For the last five years, he wasn't in its constant company.

He knew that he shouldn't be _this_ distracted. It was ridiculous really. Absolute hokum. As much as he tried to repress everything, his mind wouldn't stop relentless questions. It kept asking him when she'd contact him. He figured that she needed a few days at most before she knocked on his door, prepared to explain herself. But, he had not heard one word from Amy. No phone call, no text message, no email, no Skype call. And of course no visit. Nothing.

The only thing that kept him from demanding that Leonard take him to her apartment, or getting on a disgusting, germ ridden bus was the fact that he knew that she needed her space. She had said that being his girlfriend was mentally and physically exhausting, and that she needed time to step back and evaluate their relationship. He had agreed, albeit hesitantly. He _didn't want_ her to reevaluate the situation. Because his fear—that she would leave him—would become a reality. The way things were right now, it sure felt that she had left him.

He wasn't sure why this day was any different. He had woken up, stuck to his regular bathroom schedule, ate oatmeal for breakfast, arrived at CalTech to work diligently on Dark Matter, spoke to Leonard, Raj, and Howard at lunch, and when Kripke burst into this office to complain about Lord knew what, he glared at him and stated firmly not to interrupt him anymore because as the better physicist, he needed to be left alone to work. When it was time to go back to the apartment for Thai food, something stopped him. He knew it had to deal with her (there wasn't much that didn't these days, but that thought never left the safety of his mind). He wasn't romantic, so he couldn't say that it was an urge need to see her or he'd die.

It was an itch. And he _hated_ those. This itch wouldn't go away; his brain was driving him insane, even though his mother had him thoroughly tested for insanity.

Instead of placing himself in the passenger side of Leonard's car, he pulled his bus pants from a drawer of his office desk (he kept a spare there, in case he ever needed to take the bus home from work for whatever reason). The next thing he knew, he was on the bus on the way to Glendale. He sat in his seat, fidgeting during the whole ride. Thankfully, the person next to him remained silent, minding their own business. In his current state of mind, if he had opened his mouth to speak, a bunch of nervous gibberish would have spilled out.

He had no idea what to say. He thought that a plan of action was in order, and the second he sat down in the bus, he thought of multiple ways to approach the situation. But, it seemed he had reached an impasse. Despite his tendencies to prepare and organize, he knew that upon seeing her face, he would figure it out.

Spontaneity had never been his middle name, but maybe that was the problem all along. Amy had said several times that she deserved romance, something that was spontaneous. He _hated_ spontaneity. It wasn't planned; it was chaos, anarchy. He couldn't quantify it, and that drove him mad.

He sighed, knowing that he was going to get nowhere unless he gave into these irritating feelings. Liking singing Soft Kitty when he was ill, or drinking tea when he was upset, seeing her would make it all better. He just needed to _hear_ her voice. _Feel_ her body pressed against his in a tight embrace. _Kiss_ those lips that he had missed so dearly. He needed all of that. Right now.

As soon as the bus stopped moving, he was off of it like The Flash. He made his way into her apartment complex, a place he could almost call home because he had spent many evenings there for Date Night. A sudden stab of guilt hit him in the abdomen, causing an involuntary wince. Now was not the time to think about that.

After the agonizingly slow elevator ride, he took a deep breath and marched to the door marked _314_. His jaw was set and determination burned in his azure eyes. His inner Texan flared, telling him it was time to get his woman back.

What halted him in his tracks was the note that was taped to the door with his name written in her cursive print. He reached out to take it, confusion knitting his brows. With trembling fingers, he unfolded the piece of paper to read its contents.

 _Sheldon,_

 _Before you begin to wonder about this, please find the key to my apartment to let yourself in. It's located behind one of the pictures hanging in the hallway. The clue is "new swan stone." Once you have entered, you will find a DVD on the coffee table. Insert it into the disc player, and everything will be explained when you watch the video. Go._

 _-Amy_

He operated on autopilot as soon as his eyes finished skimming the letter. He raced to the painting near the elevator, internally thanking his helpful brain for its limited German; spending time in Germany as an adolescent had been beneficial after all. As soon as he read the words, he knew "new swan stone" meant _Neuschwanstein._ Sure enough, when he arrived at the painting of the magnificent castle that Disney had emulated for its famous image, his fingers wrapped around a key taped to the wall behind it.

As fast as his long legs could carry him, he dashed back to Amy's apartment. With unsteady hands, he jammed the key into the door and pushed it open.

The apartment was oddly cold, making him tug at his windbreaker absentmindedly. His eyes scanned the length of the room, finding that it was spotless—nothing was out of place. He immediately spied the DVD on the coffee table. Grabbing it, he brought it closer to his eyes for inspection. It was just a plain silver disc, but whatever was on it was apparently vitally important.

He did as he was told and turned on her TV to insert the disc into the player. Her face popped up the screen, startling him for a second. He took a moment to take in her appearance—one that he had not seen in what seemed like forever. Her haunting green eyes stared back at him, but there was no light in them, just a deep sadness. Her pin-straight, chestnut colored hair lacked its usual shine, and her rosy lips, which were normally tilted up in a small smile, were pointed downwards in a frown. The state that she was in reminded him of that dreadful Skype call two weeks ago.

He shuddered at the memory, momentarily distracted from his task. He shook himself out of his tangent and took a hold of the TV remote to click _play._

Sheldon's breath hitched as Amy's face unfroze.

"Sheldon," she began quietly.

He found himself digging his fingers into the upholstery of her sofa, shoulders tensed in anticipation for what she was about to say next.

"At this point, you're probably wondering why you're watching this. Why would I go through all of this trouble when I could just talk to you?" She paused to look away from the camera, seeming lost in her thoughts.

He almost wanted to turn off the video and not hear the rest of her message. There was a large part of him that _feared_ what she wanted to tell him. But, a bigger part knew that he had to at least give her the benefit of the doubt. He had spent enough time ignoring her needs, in favor of his own. This time, he would let her have the floor. A small sliver of hope bloomed in his chest. Perhaps what she had intended to say would be positive, after all.

With bated breath, he allowed himself to keep watching.

After a few seconds of silence, she spoke again. "As you may have noticed, I haven't contacted you in the last couple of weeks. I needed time to think on my own. As much as it pained me to keep my distance, I knew the second that I heard your voice or saw you, I would crumble into nothing. And I couldn't let that happen. I have more dignity than that." Her voice grew in strength; she appeared less shaky and frightened than she had when she began.

"I know that this 'break' has caused you discomfort, as it interrupts our normal interactions. For that, I apologize. On the other hand, this 'break' has taught me many things. One of which is, despite the affection I have for you, I _deserve_ better than this."

She drew in a quick breath, arching one of her eyebrows in a way that said, ' _Don't you dare refute my point.'_ It reminded him of the expression that flitted across her face when he was about to insert a blunt comment. The arch in her eyebrow disappeared a second later, giving her the same grim look.

"Before you begin your rebuttal, please let me finish. You have given me so much over the years, Sheldon. Not only have you given me your companionship, but you have also shown me how to love and how to trust. And you introduced me to a group of wonderful people. For the first time, I have friends." A brief smile crossed her lips.

"I cannot thank you enough. But, that doesn't mean I deserve the pain that comes along with being your girlfriend. While you have made improvements with reading facial cues and understanding emotions, there are times when your ability is still lacking. It's not that I don't notice the snide little comments you make about me; I just choose to ignore them because I've had to ignore my peers' remarks during my whole life. Whether the comments are coming from you, or from the people I used to know, they're still _hurtful_. I deserve better than that. And I know how hard you've worked to change for me. Believe me, your progress is admirable. That doesn't mean there aren't things I long for. Five years have passed, and even though we have exchanged _I love you's_ ,applied for an expedition to Mars together, and had our first sleepover, there are parts of the relationship that are missing. I know what you're thinking—it's not the intimacy I'm referring to. As much as I would love to have a physical relationship with you, I understand the difficulty with that. You're not the only one who has hesitations. Before I met you, there was no need for me to look at anyone that way. Yes, I hint at it often, but there's much more to it that you are unware of." She swallowed.

"In order to be intimate with you, I need to know that we belong to each other—that you are unconditionally mine and that I am unconditionally yours. No 'ands' 'ifs' or 'buts.' And I don't know that for sure." Her voice cracked at this statement. "You're a flight risk—we both know this. You're changing, I realize. But, there's still something that's blocking us. A wall, if you will. I'm on one side of the wall, and you're on the other. This wall…it's like we've come to a stand-still. To be honest, I don't know if you're willing to climb over it. And I don't know if I'm strong enough to." She sighed, her green eyes shining with unshed tears.

With a shuddering breath, she said, "After two weeks of deliberation, I've come to a decision. You may expect me to drive to Pasadena, admit I was wrong, and beg for your forgiveness. You may believe that I will ask that we pick up where our relationship left off because _of course_ you're right, and that as usual, I've let my feelings control the rational side of my brain. Unfortunately, my decision is not going to skew in your favor. As difficult as this is to say, it seems that I need more time away from you, Sheldon. Far away from you, where my head is clear and my heart isn't bruised."

The last part came out softly, and it wasn't lost on Sheldon that there was pain emanating from her voice. A spike of guilt pierced his midsection. Nevertheless, he forced himself to keep his eyes trained on the screen as she went on.

"A year ago, you left on a train because you needed time to discover how you would handle all of the changes in your life. Call it hypocritical, but I'm doing the same. This time, it is my journey of self-discovery. Please do not think this is just about you. It's so much bigger than that. As soon as I left your apartment after our anniversary, I realized how much had changed over the years, and how much hadn't changed. It scared me to think about the time before I met you and our mutual friends. While I'm grateful that I've come so far, I occasionally wonder what life what have been like if I hadn't been on the dating website that Raj and Howard had signed you up for. Life then was simpler, albeit more lonesome." She shifted in her seat, clearly agitated.

"My point is, I need to rediscover who _I a m,_ without you and without everyone else. It's time that I evaluate who Amy Farrah Fowler is as a person, not just an addition to the group. Instead of riding various trains like you did, I'm traveling by plane and by car. I have certain destinations in mind, and when I visit them, I hope I can find my answers. I already spoke with the administration, President Siebert, and the faculty at CalTech. They have allowed me to take a sabbatical for six months, and if need be, longer than that. I told them that I'd be continuing my neurobiological research, and wherever I had planned to travel, there would be access to lab equipment. They took my word for it, after I signed a mountain load of paperwork. I'm expected to publish all of my findings, which should be interesting." The tiny smile was back, if only for a few seconds.

"The administration gave me permission to leave my car at university, but the key to the ignition is with me. So, don't think about breaking in and attempting to drive it." Her voice was stern, but there was a hint of laughter underneath if one listened close enough. She paused, and in a softer tone, she forged on. "I packed most of my things because I honestly do not know how long I will be gone. If you enter the _Tardis_ doors to get inside of my room, you'll notice that my belongings are missing. For the sake of space, there were some things I didn't take with me. But, there are particular items that I would like back in your care. You can find them on my bed, in a small box with a note attached."

Her eyes began to tear up in the next moment, leaving a wet trail down her cheek. Reflexively, he wanted to wipe the tears away with his thumb. He suppressed a shudder; years ago, he didn't want anything to do with touching another human being, much less dealing with their bodily functions or secretions. He had his own to deal with, after all. He tore himself out of his reverie, waiting for her next statement.

In a strangled, choked voice, she said, "Sheldon, my decision wasn't easy, but I really believe it's the right one. If you love and respect me, please do not contact me while I'm away. Even if you try, I will block your calls and text messages. I need to do this on my own, _without_ you. And please don't attempt to see me. I'm not disclosing any of the locations to anyone; they are my own private destinations that mean something to me. I _promise_ you that I will be all right. I strategically planned this journey out, so I know how each step will be executed. Above all, I am a neurobiologist who is used to running experiments and following protocol. The method is already in place, but the results are inclusive. I need to carry this experiment out, if only for me."

With one last heaving sigh, she whispered, "I love you, Sheldon. It's frightening to me how much I love you. But, I'm not sure that's enough to keep us together. I'm sorry. I hope you understand."

The video clicked off then, leaving static ringing in the air.

He blinked at the screen before grabbing the remote to turn the TV off.

For the second time in his life, his mind was silent. The first time had been when he had received the news that his Pop-Pop had passed away. Even though he was five at the time and his mind wasn't as full of information as it was now, it still operated on a constant energy and a hungerfor more knowledge. There were always a million thoughts circling in there, never quite at rest. So, when his mother sat him down to let him know the tragic news, he was at a loss. Never had his brain quieted like it had in the moment. Now, as he sat motionless on the sofa, he felt like he was five all over again.

Eventually, his muscles moved on their own, and he soon found himself outside of her door. Blinking again, he raised his hand to knock three times and chant her name. Just before his hand made contact with the surface, his brain finally seemed to wake up from its fuzzy state.

 _Sheldon,_ it toned ominously. _Don't be a fool. She isn't there. You don't have to knock._

Taking a hold of both _Tardis_ doors, he pulled them open. He shouldn't have been surprised by the sight—she had said that she packed nearly all of her belongings. Still, the one time that he had actually ventured into her room (when he was dressed as Doctor Who), was enough for him to know that there was a quiet, intimate feeling about it. Now, it just felt cold. Unwelcoming. Empty.

The box was indeed on her bed, just as she had said. He approached it carefully, appearing as if he was afraid to touch it. When he reached the foot of the bed, he peered inside of the container. The sight of the items was enough to make him grimace.

On the bottom was the ornate wooden tea box he had given her for their fourth anniversary. As much as he loathed giving gifts, he knew anniversaries were milestones in relationships. With much prodding from Penny and Bernadette, he had relented and gone shopping. After several days of wandering through various stores, he had given up and taken to browsing online. He happened to come across a website that specialized in tea accessories. It made perfect sense to him: many of their interactions involved drinking tea, so he figured he might as well go with that. Upon receiving the gift, her green eyes had sparkled with happiness, and before he knew it, she had leaned in and planted soft kiss on his lips. After that, he realized that perhaps gift giving wasn't so horrendous after all.

On top of the tea box was the collection of _Star Trek_ DVDs he had dropped off at her apartment soon after she and Wil Wheaton had that _Fun with Flags_ argument. His grimace deepened. She really was upset with him if she was going to give those back. No one would ever want to return _Star Trek._ It was inconceivable.

His eyes kept searching the contents of the box. Tucked beside the tea box was the mushroom log he had given her. He remembered that she had complained about it at first, but grew to adore it because of its uniqueness. The reason why he was opposed to giving her flowers (especially roses—how cliché) was because they died within a few days. Mushrooms, however, could last a very long time. Why would someone want something that would sit on a table and just wither away? He didn't understand. Plus, mushrooms could be eaten and she liked the taste of them. In his opinion, the mushroom log trumped flowers any day.

His heart nearly stopped when he saw several DVD versions of _Fun with Flags._ They had agreed that after filming, she could develop copies for herself, while he was content with watching the episodes online. Despite their creative differences, Sheldon cherished his time with Amy when they had worked on videos. He liked sharing the experience with someone, and it was all the better that it was Amy. To see those DVDs in the box—it felt like a slap in the face. It hurt to think that she didn't appreciate the time they had together on something that was so important to him.

He felt another stinging sensation when he found the letter he had given her for Valentine's Day a few years ago—the one that made her his emergency contact at CalTech. After struggling for days to find a suitable present, he finally came to the conclusion that as long as it was personal and involved him, she would be content. Additionally, he had mentioned that if he were to suffer from any injuries, or impending diseases, she would be the one he'd like share the experience with.

But, the last two items, which rested innocently on top, made an unintentional whimper of misery escape his mouth. Because, right in front of him, was a frame that held their prom picture. In the photograph, his eyes were closed as he smiled goofily at the camera, while she clutched onto his arm and stared up at him, completely enamored. It wasn't the picture itself that caused him to have such an adverse reaction, as it was the memory that came along with the picture. It had been the night that he had admitted out loud that he loved her. He was terrified to tell her, but when he interrupted her rambling to mention the notion, he found a responding warmth in her eyes that told him it would be all right.

The other item, her tiara, mocked him from its spot. It glimmered in the light, reminding him of the day he had purchased it for her. They had just begun dating, and tensions were already high. She believed that he didn't care about her accomplishments (which, admittedly, at that time, were menial to his own). In order to appease her (and because Leonard had suggested it), he bought her a piece of jewelry. The moment she pulled it out of its gift bag, she proclaimed that she was a princess and suddenly, he found himself with an armful of Amy. He didn't like to admit it, but seeing her in that tiara, her eyes alight with sheer giddiness, made something flutter inside of his stomach. He had been told those fluttery feelings were called 'butterflies', but his logical mind knew that couldn't be the case. Regardless, that feeling stayed, and ever since that day, she was his princess, loathe as he was comment on it.

He noticed that the tiara had a note attached to it, like she had mentioned in the video. He took it from its resting place, unfolded it, and began reading.

 _Sheldon,_

 _Here are the items that I want you to have back in your possession while I'm gone. Please take care of the items for me, and do not dispose of them. Even though I debated on whether or not to include the tiara, I finally deemed that it was necessary. I am no longer your princess. At least for the time being. I'm sorry._

 _-Amy_

When he finished reading the last line of the note, he wordlessly folded it in half and returned it to its place in the box. Operating on autopilot again, he took the box into his arms and left her bedroom, closing the doors on his way out. Once he arrived into the main living area, he balanced the load in one arm and swiped the key from the table with the other. He gave one last glance around her apartment before quietly exiting and locking the door behind him. Slipping the key into his pocket, he made his way to the elevator. If he hurried, he could catch the next bus to Pasadena.

On the journey back to 2311 North Los Robles, as Sheldon clutched tightly onto the box, he felt a throbbing pain in his chest. It was an undeniable ache, one that lingered. If he had not experienced it before, he would have thought he was having a seriously medical emergency. He thought back to the other time in his life when he felt this way, his eidetic memory supplying him with the full details.

 _Five-year-old Sheldon Lee Cooper had spent the day memorizing the elements of the periodic table. He had already finished the school work he planned to accomplish that day during the wee hours of the morning, so he allowed himself to have fun for the whole afternoon. And of course, the periodic table board game that he begged his mother to buy him beckoned for him to play with it._

 _What troubled him was that his mind was having trouble focusing on the elements. Earlier that week, his mother had told him that his Pop-Pop passed away. Since then, he tried to block it out of his mind, as if the event had never occurred. Something in him knew better, though. His chest constantly felt constricted. It seemed to him that matter how much oxygen was actually available, it never felt like was enough. He would have preferred numbness over this feeling. Whatever it was._

" _Shelly," Mary Cooper said softly from the kitchen. "It's time for bed soon. Come get your warm glass of milk."_

" _Okay, Mama," Sheldon answered, climbing down from his spot on the wooden chair at the dining room table. He ambled to the kitchen and stopped in front of his mother. His small hand reached for the glass, but Mary held onto it._

" _How about we go into the living room, instead of the staying in the kitchen? I'd like to talk to you."_

 _She frowned. Even though Sheldon had a difficult time reading facial cues, he knew that frowns were considered negative expressions. His own eyebrows scrunched up in puzzlement, but he followed silently. Settling down in his designated seat on the couch, he held his hand out for his milk._

 _Mary carefully passed him the glass. He began to take small sips, relishing the taste of the warm liquid. After a moment, he turned his attention back to his mother._

" _What's wrong, Mamma?" he asked._

" _Shelly," she murmured. "Nothing's really wrong with me. I'm worried about you. I know that it hasn't been easy with the loss of Pop-Pop. I've noticed that you're a little more off than usual."_

 _Not one to drink a beverage and talk, Sheldon set his glass down on coaster resting on the coffee table in front of him._

 _He paused, contemplating the method in which to answer. Finally, he said, "I try not to think about it. Whenever I do, my chest hurts really baldy, and I don't know why." He shrugged, but it was obvious that not knowing the answer truly bothered him._

" _Oh, Sheldon." She inched closer to him, opening her arms. "Come here."_

 _Resolutely, he shook his head. Despite the fact that he loved his mother dearly, he didn't like the idea of touching anyone. The thought of physical contact was enough to make him shudder. He tried to avoid it at all times, except for when he had no other choice. Luckily, even when he was forced into it, he kept emergency Purell hidden in his pocket._

" _Sheldon Lee Cooper," she responded, sternness evident in her voice._

" _Fine."_

 _He begrudgingly moved and sat down in her lap. Before he could register anything, she wound him in a tight embrace in her arms. He didn't want to say anything, but his mother's proximity was always comforting._

" _I'm so sorry that you have to go through with this. I know it's your first time dealing with death, and I'm sorry to say that it doesn't get any easier. But, I can help you understand why your chest hurts." Her hand gently stroked his cheek in an affection matter. "That pain you feel…it's your heart breaking," she whispered, her soothing Southern drawl filling his ears._

 _Despite only being five, Sheldon knew it was improbable that a heart could break. A heart was a muscle, and while muscles were capable of aching, recovery was still possible. Muscles weren't like glass—they couldn't break. He didn't understand what his mother meant, so instead of trying to reason with her, he let her hold onto him._

Years later, as Sheldon nearly reached 4A with a box of Amy's belongings in his arms, he finally understood what his mother was getting at that day. His heart couldn't physically break, but metaphorically speaking, yes it could. That ache—it was shattering.

His heart was breaking, and he wasn't sure if there was anything to do to make it stop.

* * *

 **May 21, 2015**

Amy scanned the large monitor attached to the wall to confirm her gate number. She was always a bit paranoid when it came to air travel. It involved much more planning than simply taking off in a car. There was a right place and a right time, and from her own experiences, she knew missed flights were the worst.

Once she located her destination and found the corresponding gate number, she nodded, breathing a silent sigh of relief. Fortunately, _A-27_ wasn't very far from where she currently was. Even though security had taken longer to get through than expected, at least it ended near the _A_ gates.

Wheeling her small carry-on bag behind her, she strolled across the floors of the _LAX_ airport. While she walked, she remembered that she had to make one phone call before departing. Fishing her mobile out of her purse, she dialed the number that she now knew by heart.

The person picked up on the second ring.

"Amy! Are you okay? Is everything all right?"

Amy could hear the exasperation on the other end of the line. _She must not have started drinking yet,_ she thought silently. _Otherwise, she'd be a lot mellower._

Cringing, Amy said, "Hi, Penny. I'm okay. Just got through the security checkpoint, actually. I'm on my way to the gate. The plane is due to board soon, but before I left, I just wanted to let you know that I'm fine and that everything is going well."

Penny sighed. "You're really going through with this, huh?"

There was no hesitation as Amy responded.

"Yes. I have to do this for me. You let Sheldon go on his own a year ago, and he didn't even have a plan. I do. I know where I need to go, and I know what I need to do. I promise that this is important, Penny. Trust me."

"I do. And I'm really glad that you decided to tell me before anyone else. Thank you for calling me before you left." She was quiet for a moment. When she spoke again, there was a hint of melancholy in her voice. "I'm going to miss you, bestie."

Amy stopped where she was. That was the first time Penny had called her that. Sure, she had mentioned the pet-name to Penny many times, but never once did she receive the sentiment in return. Her lips curled into a sad smile. This must have been how Leonard felt when Penny said she loved him for the first time.

"And I you."

"Take care of yourself, Amy. I know you said that you can't keep in contact because you want to do this on your own, but if anything happens, please let someone know. No one knows where you're going to be, and naturally, we're going to worry. We're here for you. All of us."

Amy nodded, even though she knew Penny couldn't see her. "I know. Thank you. Oh, there's something I need to ask you before I hang up."

"Yes?"

"Would you mind looking after Sheldon? I know he'll be okay with this eventually, but for now, he may be a little shaken up. It's just—a lot of people have left him, and even though I feel guilty for being of those people, deep down, it's for the best. I want to make sure that there's someone there in case...anything happens to him. Can you do that for me?

"Of course. Leonard and I will keep an eye on him." She paused. "He loves you, you know. In his own Sheldon way."

Amy sighed softly. "I know. I love him, too. And that's why I have to go."

"Good luck. I'll drink a glass of wine in your honor."

Amy had to suppress a chuckle. "Thank you. Bye, Penny."

"See you later, Amy."

She pulled the phone away from her ear to end the call and toss the device into her purse. She was about to reflect on her conversation with her best friend when she realized that she should probably check the time. Glancing at her watch, her eyes widened and she quickly scurried the rest of the way to the gate. By the time she reached it, pre-boarding had started. She barely had enough time to collect herself before her zone number was called.

Clutching onto her boarding pass, she looked down at it and back at the monitor behind the woman at the counter to ensure that she had ended up in the right place.

 _Springfield, Illinois_ stared back at her from both the page and the screen.

"Boarding Zone 2," came the voice from the intercom.

She stepped into line. Under her breath, she murmured to herself, "Looks like I'm ready to go home."

* * *

 **A/N:**

 _If you'd like to let me know what you thought, please leave a review. It's much appreciated. Also, if you are wondering, the chapter title is based on Shakespeare's line, "Parting is such sweet sorrow." I'm a big fan of Shakespeare, so don't be surprised if he somehow gets woven into the story._


	2. Mirroring Emeralds

**A/N:**

 _I promise I haven't abandoned this story. I'm so sorry it's taken me this long to post an update. If you've read some of my earlier work, you may know that I tend to write as I go along, which usually means slow updates. Finding the time and the motivation to write has been incredibly difficult lately, but I finally managed it. I fully intend to finish "The Caged Bird Hypothesis" from beginning to end. It just might take a while. This was going to span across the hiatus, but it will lapse into Season 9. Please disregard the events that will occur on the actual show (if you've read the taping reports, then you know what I'm talking about)._

 _Anyway, I hope you enjoy Chapter 2. I apologize for the lack of Sheldon in this particular chapter, but he will come up later on. The spotlight will mostly be on Amy from here on out. There may be some typos or errors here and there. I got tired of reading the same lines over and over again while editing during the wee hours of the morning._

 _Thank you so much to all of the people who have read this story and left reviews. You guys are awesome._

 **Disclaimer:**

 _If I owned The Big Bang Theory, I'd be the happiest person alive. Alas, that is not true. It's all Bill Prady's , Chuck Lorre's, and CBS's property._

* * *

 **The Caged Bird Hypothesis**

Chapter 2 **:** Mirroring Emeralds

"Parents can only give good advice or put them on the right paths, but the final forming of a person's character lies in their own hands." –Anne Frank

* * *

 **May 22, 2015**

Looking up, Amy swallowed thickly.

In front of her stood her mother's Victorian home, in all of its ancient, beautiful glory. With its thick outer walls covered in ivy and painted in a deep maroon with white trim, antique interior design complete with ornate furniture and overall old-fashioned ambiance, it never ceased to make Amy feel like she was living in the nineteenth century.

Its presence used to be a source of comfort.

But now, as she remembered why she was there, the feeling of safety quickly vanished and was replaced with a hollow type of sorrow.

With a shuddering breath, she wheeled her suitcase in one hand and her carry-on with the other. When she reached the front door, her hand grabbed the brass knocker. She tapped it loudly against the door. The sound of shuffling feet from the other side notified her that her mother was indeed home.

The door clicked open to reveal a petite woman in a long khaki skirt and navy blue sweater. Her light brown hair, tinged with a bit of gray, neatly brushed against her shoulders. Gentle brown eyes stared back at Amy behind a pair of black round glasses that perched on the bridge of woman's nose.

"Amelia," Maria Fowler said quietly.

"Mother," Amy greeted. "I hope you were expecting me. I did call."

"Yes, dear. I recall that conversation. Come in."

As soon as Amy crossed the threshold, she gazed around her.

Everything was just like she had remembered it. Nothing had been added or removed; not a piece of furniture was out of place. Her mother was never a person who liked to change things once she had solidified in her mind that was how she wanted it.

Amy had to bite her lip to keep from snorting. It sounded like someone she knew.

"I was just about to have tea. Care to you join me once you to settle in?" Amy's mother asked, gesturing to Amy's bags. "I assume you would like to place your belongings in your bedroom. And before you ask, it is just how you left it. The only thing that I did was maintenance in the lab for you."

Amy nodded. "I would love some tea. Thank you."

As she maneuvered her bags in the direction of her room, Amy had to suppress the urge to cringe. Having just spoken with her mother and feeling the waves of awkwardness that passed between them, she now understood why she was so socially awkward around people. She supposed she hadn't realized just how…influential her mother was on her social skills. It wasn't until she had made actual friends that it dawned on her that when she first met them, she was probably a fish out of water.

For as long as she could remember, her mother had been the only one she could talk to. And it wasn't like the elder Fowler was much of a social butterfly. Conversations between the Fowler women were limited at best. They mostly became absorbed in their own interests, and only talked about the thing that they both cared about: neuroscience. While the topic of neuroscience was certainly enough to keep Amy and Maria going for a few hours, eventually, they tired of it and silence overtook them once again.

Growing up, Amy was used the comfort (and loneliness) of silence. And it seemed like she was about to return to that life, at least of the time being.

When Amy reached the door of her former bedroom, she hesitated. It had been _years_ since she'd last visited. She wasn't sure how she would feel.

Her room had been her sanctuary from the time she was an infant until she left for undergraduate school. Amy had spent many days alone inside of this room, reading medieval literature, listening to folk music, writing her own poetry, or working in the laboratory that her mother had designed and built for her.

She was definitely surprised that the lab had been maintained. She had fully expected it to be cleaned out entirely, but it was a relief that it was still there and functioning. She had promised CalTech that she would take her sabbatical to continue with her research, and having a lab handy at home was perfect.

With a deep sigh, she pushed open the door, the feeling of nostalgia washing over her.

The room wasn't complex, but Amy preferred its simplicity.

The walls were painted a mossy green to represent the trees in a forest, while the ceiling was a light blue to match the color of the sky. As a child, Amy had wanted the feeling of being in the forest without having to actually leave her small paradise.

Smiling, she glanced at all of the posters that remained tacked onto the walls. Most of them were science related, but she managed to find some that were Medieval themed. Her gaze shifted to the large wooden desk that was pushed against the wall closest to her. She loved that desk for its delicately carved edifice. It looked like it was about a hundred years old, but it still stood as strong as ever. Amy could imagine when she was younger, sitting at the desk, with the lamp on, writing her worries away in her diary.

She cast her gaze towards the full sized bed that rested against the opposite wall facing her. It wasn't a water bed, but the cushiony mattress was similar to that of one. As a child, she never had any issues falling asleep. Her bed was a comfortable oasis that could easily whisk her away into Dream Land.

In the center of the bed lay her white stuffed teddy bear. The bear, with his kind brown eyes and arms surrounding a plush red heart that said, _Be Mine,_ was her childhood friend _._

She had bought Snuggles after passing by the window of _Hallmark_ on her way home from school during the seventh grade. It was Valentine's Day, and she would be lying if she said she hadn't spent most of it hidden away in the library, shielding herself with a book so the other kids didn't know she was crying. She hated how every girl seemed to have valentine, even the extremely quiet ones who looked like they couldn't talk to a boy to save their lives. Feeling sorry for herself that day, she caved and purchased the bear because that was the closest thing she would have to any type of romance.

Amy's thoughts spiraled back to the present time when she felt her heart clench painfully in her chest. Seeing Snuggles for the first time in years reminded her of her own Cuddles. He was back in Pasadena, probably working on solving the next biggest physics crisis, too busy to think about her at all.

Shaking her head, she mentally scolded herself for thinking about him. The point of leaving was to put him aside for now so that she could focus on herself.

"Maybe seeing the lab will help," she muttered.

She plopped her bags on her bed and walked to the back of the room where a single door was shut. Without hesitating, she yanked the door open and flipped the light switch on.

Amy stared at the large laboratory and smiled.

This was the lab she had used as a child and adolescent—where she first had the opportunity to design and run experiments, examine specimens under the microscope (especially brain matter), and overall enforce her love of all things science related.

While it wasn't as high-tech as the one at CalTech, it was similar to the first lab that she worked in before she transferred to the university. There were a several beakers, graduated cylinders, and other glassware hidden in the cabinets. High gadget technology sat on the counter tops, all shiny and freshly cleaned. There were even a couple of cages that normally contained animals that Amy could experiment with as she pleased. They were, of course, devoid of any living creatures at the moment. But, her mother had connections, being a retired neurosurgeon and a current professor at a local university. If she needed lab animals, all she had to do was ask.

Amy decided to run her fingertips across the surface of the counters. She only really felt completely at home when she was in the lab. It was just something about working under the lights, scrutinizing whatever neurobiological thing she was working on at the time.

A soft knock on the door pierced the silence in the air.

Amy turned to find her mother leaning against the door frame.

"The tea is freshly brewed, Amelia. Would you like to join me now?"

The younger Fowler nodded. "After you, Mother."

Maria exited, followed by Amy.

She closed the lab door behind her, mentally reminding herself to spend the remainder of the evening locked inside of there. She could do some preliminary work that didn't involve examining addiction levels of primates, or stimulating the nervous system of sea stars.

It didn't take long for Amy to reach the formal sitting area. She elected to sit down on the high backed Victorian chair that looked like something one of the former Queens of England would have perched on for tea.

She noticed the silver tray on the coffee table. The tray, the kind that women of wealth used to have their servants carry, was covered with fine white china that had tiny pink roses dotting across the surfaces. A steaming tea pot was in the center of the tray, with two cups and matching saucers on either side. Additionally, two sterling silver spoons, a bowl for sugar cubes, a plate for lemon wedges, a small glass jar of honey, and plate of what appeared to be butter cookies were all neatly placed on it.

"I brewed a combination of chamomile and peppermint rose tea. I thought you needed something calming," Maria said, settling herself down on the loveseat, opposite of Amy. She gestured to the tray. "Help yourself."

Amy felt touched. For as few words as Maria actually uttered, her actions spoke volumes.

"Thank you, Mother."

Amy carefully poured herself a cup of tea. As soon as the liquid escaped its china container and dripped into the cup, its aroma immediately soothed her tense muscles. After squeezing in a bit of lemon and adding two sugar cubes, she brought the cup to her lips, taking a sip of the scalding beverage.

When Maria situated herself with her own tea, she asked the question Amy had been dreading to answer.

"Amelia, tell me the real reason why you've decided to visit. I do not believe that you are simply here to see me, as much as I wish that were the truth."

Amy sighed, took another swig of the tea, and placed it in its original spot on the silver tray. She leaned back in her seat and glanced up at the ceiling to avoid her mother's probing gaze.

Shrugging as if it wasn't a big deal, she said, "I needed to get away. Life in Pasadena was suffocating me. Work became stressful, so I asked to take a sabbatical."

Even though Amy couldn't tell what Maria's facial expression was, she could imagine her mother quirking an eyebrow at her.

"You know that's a bold-faced lie, Amelia. Tell me the truth."

Amy winced. That was the _Mom Voice—_ the one that all mothers used when they wanted information _now._

"Fine." Amy frowned, straightening her posture. "It's—it's about Sheldon, okay?" she paused, swallowing around the sudden lump in her throat. "We're on a bit of break. I felt that if I came home, I would be far enough away to think clearly."

Maria flinched. "Ah, I see." She trained her eyes on her beverage and continued to drink in silence.

At that moment, Amy wanted nothing more than for the floor to open up into a gaping hole and drag her down into its depths. She and her mother never discussed their feelings. The endeavor was always way too awkward, so they mutually agreed that neither would participate in such a thing.

Amy was torn from her thoughts when she heard her mother clear her throat. Looking up, she found a gentle expression on her face.

While Maria was never a harsh person, she certainly wasn't one to openly show emotion. To say Amy was a little startled would have been an understatement. And the words that came out of her mother's mouth surprised her even more.

"Amelia Farrah Fowler, it is perfectly normal to be upset about a situation like this. You don't need to always have such a brave face."

Amy's shoulders sagged. She couldn't get much past her mother—she knew her better than anyone else.

"What choice do I have? If I don't act like I'm okay, then what am I supposed to do? I decided to leave on my own; no one forced me to. I thought it was the right decision. Despite what you may think, I didn't leave solely because of Sheldon. Yes, he has a large part in this, but I also figured out that I was losing who I was in Pasadena. Somewhere along the line, I started to realize that I was melding into _that_ group. I got caught up in their lives, all too enticed by the prospect of friendship. Because of that, I neglected to see the parts of me that were slipping away."

Maria's eyes flashed with concern. "What do you mean by your statement? I'm not sure I quite understand."

A long, drawn out breath left Amy's mouth. When her mother asked her to have tea, she expected polite small talk, followed by awkward silence. Not an interrogation.

"I'm not as strong and independent as I used to be. Before I had friends, I didn't need to rely on anyone. I may have craved company, but I wasn't on my hands and knees begging for it. Now that I've had a taste of what true friendship is like and have seen the beauty of it, I don't know if I can give it up." Amy's eyes widened at the realization. "Now I know how the monkeys feel in the lab. I'm the product of my own addiction study—I'm addicted to the company that my friends provide."

Maria sipped at her tea, allowing Amy to momentarily revel in her epiphany. After a few moments, she chimed in.

In a quiet, but sterner voice, she said, "And the problem with being 'addicted to your friends' is what? You've always wanted friends. That's all you could talk about as a child. Now you have them and you're complaining?" She shook her head. "That's very contradictory. Amelia, get to the root of the problem. You are beating too much around the bush. I cannot decipher what it is you are trying to tell me."

Amy groaned, removed her glasses, and proceed to rub at her eyes with the heels of her palms. She was trying to buy time to further evade the question, but of course, she knew she couldn't avoid answering. Her mother could definitely be an insistent woman when she wanted to be.

Pushing her glasses back on her face, Amy squared her shoulders.

"It's not that I don't love having friends. I really do. It's just that I'm afraid that I miss the old Amy Farrah Fowler. The one who was quirky and broke social norms. The one who was so emotionally strong that not even a cruel comment could truly break her down. The one who didn't need to constantly have 'Girls' Night' to make her feel better about herself. The one who didn't need an egomaniac boyfriend who keeps stringing her along. After much thought, I've decided that I deserve to feel happiness without the fear that I'm on a time crunch. I constantly feel like someday, they are going to tire of me and leave first. I'm not sure I could handle the rejection. I haven't stood on my two feet in such a long time because I've been leaning on other people. The old me wouldn't have done that. I need to figure out if she still exists. Do I want her to? I don't know. That's why I'm here, and that's why I'm traveling around this country. This is for _me,_ Mother."

A rare, full blown smile crossed Maria's lips.

"You remind me so much of your father sometimes."

Amy's jaw dropped. Her mother _never_ talked about her father. Ever.

She wasn't even sure how to reply.

So, she sat in silence, with her mouth hanging open, looking like a gobsmacked fool.

Maria clucked her tongue impatiently. "Amelia, do close your mouth. I assume you do not wish for flies to nest in there."

Amy snapped her mouth shut. But, surprise and confusion still swirled in her emerald eyes.

Luckily, Maria understood what her daughter wanted to say, despite the lack of words.

"I realize I don't generally talk about your father, but he did exist. We were a married couple who was very much in love." Nostalgia glistened in Maria's eyes.

Amy reflexively clutched onto her the upholstery of her seat. When she spoke again, she had to fight to keep the hysteria out of her voice.

"I was aware that I had a father because biologically speaking, it makes sense. But, I didn't know that you involved with him. You led me to believe that you had just gone to an intelligent sperm bank. You said you wanted a child, but didn't want to spend the rest of life as a married woman. There are no family photographs with him. There's no trace of him. I didn't know—"

"Yes, that's what I wanted you to believe," Maria interrupted. "I thought it was easier than telling you the truth. When you were a child, I didn't want you to become entranced by the idea of finding 'true love.' That was why I prohibited you from watching any of those Disney movies. There was no way that I was about to let my daughter get into her head that all a woman needed in her life was a man to save her. I learned to save myself, and that's what I intended to teach you. I kept your father a secret because if you had known that I was in love once, then…"

"Then I would believe that it was acceptable for me to feel it as well," Amy finished roughly. She threaded her fingers through her hair impulsively, yanking on the tresses in frustration. Her heart beat wildly in her chest, as her cheeks flushed a deep pink. Her eyes suddenly became misty.

"I can't believe you kept that from me! Mother, do you know how many nights I've dreamed about having a father who could read me bedtime stories, hug me when I was feeling depressed, and ruffle my hair after I did something he was proud of?"

"I am aware, and for that, I apologize." Maria paused, shame coloring her tone. "It was for your own protection, which is something I'll have to explain in more detail later on. I understand that we have a lot to discuss, and while you are home, I hope we have a chance to do that. Whatever questions you have about your father, I will answer, no matter what they are. It's time for you to learn about the other half of you. If the purpose of your traveling is to rediscover who you are, it's only reasonable that you understand your heritage."

Amy took a shuddering breath. "Before we even delve into the topic of my father, I need to ask you something."

Maria set her empty tea cup on the coffee table, crossed her legs, and placed her hands in her lap.

"Yes?"

"If you wanted me to avoid love for so long, why did you make me vow to date once a year? I don't understand."

A quiet chuckle unexpectedly bubbled out of Maria's lips. "Oh, Amelia. That was your grandmother's doing, not mine. I was more than happy to let you stay single. However, my own mother was concerned for your well-being. You know Grandmother Evangeline and how traditional she is. She was afraid that you would never attract a gentleman. She noticed how you were constantly alone, which did not settle well with her. She didn't want you to grow old without someone there beside you. In other words, she didn't want you to turn into me." Maria smiled ruefully.

"She told me to set you up on those dating websites, but coerced me into making it seem like it was my idea. The last thing she wanted was for you to become upset with her. Apparently, it was perfectly acceptable in her mind for you to get frustrated with me instead. The batty old woman." She shook her head fondly.

"Against my better judgment, I followed her instructions and pushed you to 'date.' I was secretly glad that none of the men worked out for you."

Realization dawned on Amy. "So, when I actually fell in love with Sheldon…"

"I was hesitant, yes. A bit upset? Certainly. Concerned? Of course. I didn't want you to have the same fate that I had. I would never wish that on anyone, let alone my own daughter."

Amy nodded in understanding, but there was frown on her lips. A part of her was dying to know what her mother was referring to, but she didn't feel the need to press the issue at the moment.

Instead, she asked, "You never approved of Sheldon then?"

Maria heaved a slightly exasperated sigh.

"Amelia, there was never a moment when I thought he was wrongfor you. On the contrary, I believed that you had found exactly the right person for you. And that's why I was worried. I knew that if things were to fall apart, you would be devastated. Nothing is worse than losing someone that you know deep in your heart you belong with." Maria's eyes shined with unshed tears. "I know the feeling all too well."

Amy looked away, deciding that she wasn't quite ready to open the fresh wounds of her relationship with Sheldon. She would much rather talk about her elusive father.

"I want to know everything about my father." She paused. "But, please do not give me the entirety of the information tonight. It's just too much all at once."

"Of course—I completely understand. If you wish to bring up your father, then by all means, do so. It will be on your terms. But, I must apologize for inserting your father into the conversation without a fair warning. I'm not exactly sure what came over me just now. I've had practice holding my tongue all of these years. Every time you did something that reminded me of him, I chose to stay quiet. My only conclusion is that this piece of information slipped out because you wanted to know more about yourself." She shrugged delicately.

Amy shifted awkwardly in her seat, seeming antsy.

"There are a few of things I'd like to ask you right now, though, if you don't mind."

Maria nodded. "You may proceed."

"What is his name? Is he still alive? And what did he study in school?"

Maria's lips curled into a small smile. "His name is Robert Anderson. He is two years my senior, and yes, he is still alive." She stopped speaking for a brief second. Amy noticed that the smile grew a tiny bit bigger. "He was a biology major with a psychology minor. As much as he loved the sciences and the social sciences, he also dabbled a bit in the arts. He didn't like to boast, but he was actually quite a poet. That's actually how we met—I first laid my eyes on him at a poetry reading."

Amy's stomach fluttered. That sounded incredibly romantic. And so unlike her mother. She had never imagined her mother as the type to wander into a poetry reading. She was always too straight laced and serious for something so…artsy.

"You and poetry, Mother? I cannot imagine that," Amy laughed.

Maria laughed along with her daughter. "A friend convinced me to go. It wasn't my idea."

"And you actually stayed? I'm impressed."

A ghost of a smirk graced Maria's lips. "I was more open-minded when I was younger, Amelia. You have to give me some credit."

Amy could hardly believe it. She almost wanted to burst out laughing. Here she was playfully joking around with her mother. Years ago, this would have been improbable. But now…they were able to talk freely, without awkward silence. She couldn't help it; she smiled.

Maria could easily pick up on daughter's brighter mood, having felt the tension she normal shared with her dissipate. She decided to run with it.

"Would you like to see a picture of him? I have two that are hidden in my bedroom." She hesitated for a second before continuing. "I understand if it's too soon, though."

A soft look crossed Amy's face. "Yes, if it wouldn't be too much to ask. I want to know what he looks like."

Lifting herself gingerly out of her seat, Maria quietly said, "I'll just be a moment. There is one I would like to show you one tonight. The other will have to wait for another day." She turned on her heel, walking swiftly out of the room.

Amy waited in bated breath for her mother to return. She had to resist the urge to bite her fingernails in anticipation. The tick-tock of the old grandfather clock drove her up the wall; its steady rhythm had no match for her erratic heartbeat.

When her mother appeared once again with a golden circular frame in her small hands, Amy let out the breath she had been holding in. Her shoulders visibly relaxed from the stiff position they had been in.

"Join me on the loveseat, Amelia. It will be easier to see this way," Maria instructed.

In two quick strides, Amy moved in front of the loveseat and sat down next to her mother. Leaning over her shoulder, she gazed at the photograph. A whisper of a gasp left her mouth.

The man staring back at her was definitely her father. Even though the photograph had yellowed with age, Amy could tell that his eyes were a sharp, intense emerald green. They were her eyes through and through. His smile, which was somewhat crooked but still loveable, was quite similar to her own. His hair, a deep chocolate brown, appeared soft and smooth. One dimple showed on his right cheek, and the sight made Amy's heart melt a little. He was a very attractive man—no wonder her mother had fallen for him.

She glanced down at what he was wearing: a tuxedo. Her eyes widened and shifted their focus to the right side of him. He had his arm wrapped around…her mother.

In the photograph, Maria Fowler beamed into the camera wearing a lovely wedding gown. Like Maria, the dress was petite, but it was cut so beautifully on her. With a beaded bodice and flowy ballroom style finish, it certainly made her look like a princess. Her veil was thrown back to reveal her radiant face, shining with bliss.

Without a doubt, this was the most beautiful picture Amy had ever seen. With a gentle finger, she reached out to trace the image of her parents.

She felt her eyes well up with tears. "It's beautiful," she whispered, holding back a sob.

Maria smiled, setting the picture frame on the coffee table. "Thank you, Amelia. Handsome devil, isn't he?"

Amy grinned through her tears. "Most definitely. You two look perfect together."

There was wistful look in Maria's eyes. "I have to agree with you."

Hesitantly, Amy touched her mother's knee. Physical contact had never really been their thing.

"Thank you for showing me the photograph. It means a lot to me. Probably more than you'll ever know."

To Amy's complete dismay, her mother shifted and carefully embraced her. She stroked her hair as they hugged.

No words were exchanged between them, but there didn't need to be. This simple gesture was all it took to get the message across.

When they both moved away from one another a few moments later, a comfortable silence settled.

Amy smiled. "I think that's enough discussion on that for tonight. I should go back to the lab and pull up the data that I've been working on. I did tell the university that my sabbatical was going to put to good use." She chuckled. "Would you mind speaking with your contacts about lab animals? I may need to run some tests while I'm here."

"Of course. Good luck with your lab work, Amelia. I am preparing dinner tonight, so if you find yourself famished, you can find me in the kitchen. Would you like to keep the photograph in your bedroom while you are here?" With that, she picked up the used tea cups and placed them on the tray. Before she made her way out of the room, she turned to Amy. "Would you like to keep the photograph in your bedroom for the duration of your stay?"

Her answer came quickly. "I would love to."

Amy took a hold of the picture frame and cradled it to her chest. She watched her mother go, but before retiring to her own bedroom, she marveled at all of the information she had learned in one sitting with her mother—a woman who, only an hour ago, hardly exchanged words with her.

 _Maybe this trip will be better for me than expected,_ she thought to herself.

Shaking her head and smiling again, she stood and headed towards the lab in her room.


	3. Rewinding the Clock

**A/N:**

 _Contrary to what it may seem, this story has not been abandoned. I've been working on it, I swear. I have this bad habit of publishing as I go, which is probably not the best idea. A lot of authors will write a piece and publish the whole thing when it's done. Unfortunately, I'm not that organized, haha. I'm in school for most of the year, so balancing writing with academics, work, and a social life is rough._

 _I realize it's been nearly a year since I've written anything, so readers who were once interested in The Caged Bird Hypothesis may not be anymore. I understand if that's the case—I've kept you guys waiting after all. I started this story thinking that it would be over before Season 9 began. Turns out I was wrong. So much happened in Season 9 that it blocked me from having any ideas to write about. On an unrelated note, I actually got to watch Season 9, Episode 5 ("The Perspiration Implementation") being filmed live! Somehow my best friend and I scored tickets, and let me tell you, the experience is incredible. That tangent aside, I'm sincerely sorry that I haven't updated in forever._

 _I plan to finish it—it just may take a long time. Please disregard any of the events in Season 9. Amy's still away on her journey of self-discovery, and Sheldon's still at home in Pasadena. Also, I've decided to create a playlist for this story. The songs come from_ _ **The Theory of Everything**_ _soundtrack. It's a beautiful film and the music is gorgeous. I'll post the playlist at the bottom of the chapter, but for this chapter, the song that corresponds is "Forces of Attraction."_

 _Without further ado…_

 **Disclaimer:**

 _I wished I owned The Big Bang Theory, but unfortunately, the rights still belong to Chuck Lorre, Bill Prady, and CBS. I also do not own The Theory of Everything (Working Title Films does)._

* * *

 **The Caged Bird Hypothesis**

Chapter 3 **:** Rewinding the Clock

"If you reverse time, then the universe is getting smaller. So, what if I reverse the process all the way back to see what happened at the beginning of time itself?"—Eddie Redmayne as Dr. Stephen Hawking in _The Theory of Everything_

* * *

 **June 12, 2015**

"Amelia, I finished preparing dinner. Would you like to join me now?"

Maria's voice sliced through the complete silence in the lab. Amy looked up from the petri dish she was bent over and removed her goggles.

"Sure. I'll be there in just a minute."

Maria smiled from the doorway before quietly taking her exit. While watching her mother go, Amy took off her gloves and hung her lab coat on the chair.

She glanced at the cages, which now contained two rhesus monkeys. They stared at her, dark brown eyes widening as she closed the distance between herself and the cages.

"Sebastian and Aurora, I'll be back. Don't fight, fling your feces, or try to break out," Amy instructed in a firm voice, shaking her finger at them. "I was lucky enough to get you in here, so please don't jeopardize my loan."

In response, both monkeys trilled at her and gently slammed their small fists against their respective cages as a sign of understanding. Sighing internally, Amy thanked a deity she didn't believe in that she received two fairly well behaved monkeys. She had dealt with much worse, so this was certainly a true and pleasant surprise.

She washed her hands in the small sink that was near the door before making her way out of the lab in her bedroom. When she reached the formal dining area, she took her usual seat across from her mother at the oval wooden table. Two place settings were already present, including a wine glass for each woman.

Her mother carried over a large dish with a cover on it. Setting it in the center of the table next to the garlic bread, she lifted the lid to reveal spaghetti and meatballs. A serving spoon was stuck in the center, ready to be used.

Amy smiled as she watched Maria reach into the refrigerator to grab a bottle of white wine. With careful precision, Maria uncorked the bottle and poured a generous amount into each glass.

"Help yourself, Amelia." She gestured toward the entrée.

"Thank you, Mother," Amy said quietly, spooning spaghetti onto her plate.

Her stomach clenched reflexively as she thought about Sheldon and his love of spaghetti with tiny pieces of hot dog in it. She pushed the thought away, feeling disgusted with herself. Really, it was ridiculous to think of Sheldon at this point. It had been a few weeks since she'd left, and even longer since she'd truly spoken to him. She was sure that she was slowly (very slowly to be accurate) moving on. Or, at the very least, beginning to focus on other things besides the tattered remains of their relationship.

"Is something the matter, Amelia? You seem distracted."

Amy tried with all of her strength to fake a smile. She knew her mother could see right through it, but she sincerely hoped that she would just accept the façade for now and move on. She never did like lying, but now was not the time for the truth.

"I'm fine. I was thinking about my research project." She handed the spoon to her mother before reaching for a piece of garlic bread.

"Ah, I see." Maria raised an eyebrow in a manner that said she didn't quite believe her, but she didn't press the issue. "And how are your research plans?"

"Things are well. If I spend a little bit more time here, I'll be able to finish my observations, statistically analyze the data, and begin writing a journal article. I need to prepare several articles for peer reviews while on sabbatical, so this is just the beginning."

Maria adjusted her glasses primly on her nose, appearing very much like a librarian. "Fascinating." She took a sip of her wine and delicately twirled the spaghetti around her fork. "What exactly are you examining?"

Amy hesitated, afraid her mother would think her research project was stupid.

Exhaling slowly and gulping down some wine for liquid courage, Amy said, "My intent with the study is to see how the monkeys react to different stimuli. I'm measuring their serotonin, norepinephrine, and dopamine levels. Once I get a base rate, I'd like to expose them to various stimuli in attempts to drop the levels to a low point. Then, the goal would be to make the levels rise again with tactics that humans use to improve their neurotransmitter levels, such as exercise, antidepressants, fornication, and even out of the biological range, what one considers 'love.'"

"Interesting." Maria pursed her lips, but made no move towards continuing her thought.

"What is it?" Amy urged.

Maria dabbed at her mouth, placed her napkin back on her lap, and sighed.

"It's not lost on me why you're examining that particular research question. The shift is somewhat dramatic from the addiction study you participated in for months."

Amy blanched. "I'm not sure what you're referring to."

Maria's eyebrow lifted again. "You named the rhesus monkeys Sebastian and Aurora. Before I called to have them delivered for your use, they were known as Test Monkeys 1 and 2. Clearly there's a connection between their names and your situation. And you said 'love' could be used to raise neurotransmitter levels. You know as well as I do that most animals revert to biological means. They copulate to reproduce and therefore, to survive. Love hardly has any place in that circumstance."

Groaning, Amy looked away from her mother's steady gaze. "I knew you'd think this was a terrible idea."

Maria's lips straightened into a frown. "I never said that. I was merely pointing out that you are using this study to hide from your true feelings."

"Stop trying to psycho-analyze me. You sound like Leonard's mother." Amy wrinkled her nose. Even though she had never formally met Beverley, she had heard enough stories.

"I don't need to psycho-analyze you to know what you are thinking. It's evident to me that by focusing your energy on research, you are attempting to work through your own problems. I didn't say that was such a horrid thing."

Sighing, Amy ate a few more bites of her dinner in silence. Until her mother had mentioned it, she hadn't been aware of her actions. Her eyes widened as she realized with horror that there were parallels between her research and her situation with Sheldon. She silently cursed her unconscious mind for betraying her.

When she felt she was ready to talk, she pushed her plate away. She could feel her stomach roiling, not from the food, but from what she was about to tell her mother.

"Perhaps it's true that my current situation has manifested itself in my research. I can assure you that I did not choose it purposely because of that. I'm certain that my unconscious mind was involved in the process." She took a shaky breath. "It has not been easy for me—being away from him. From _them._ I miss them, even when I know I shouldn't. I'm the one who decided to leave. It was my idea, so I'm entirely to blame for this feeling of emptiness. But, Sheldon…" she trailed off for a second. "I don't want to think about him. I don't want anything to do with him right now.I thought—I thought that if I left, all thoughts and feelings regarding him would be pushed aside while I worked. Unfortunately, there's still a part of me that wonders about him. I don't know how to shut that part off."

Maria listened to her daughter intently with a look in her eyes that Amy couldn't decipher. It appeared to be a combination of understanding, sympathy, and sadness.

"Are you telling me that you wish you had never met Sheldon and established a romantic relationship with him?"

The answer was immediate.

"No."

"No?"

Amy swallowed, feeling glimmers of wetness around her eyes. "As much pain as he's caused me, I will never regret meeting him and falling in love him. He taught me that love was possible, and for that, I'll always be grateful. I still love him, despite everything." Staring at her hands to avoid looking at her mother, she said, "It completely frustrates me that I continue to harbor feelings. I really shouldn't, not after realizing that there were moments when he didn't value me as he should have. It was one thing for me to be his friend, but it was another thing to date him. When we were just friends, I didn't want more. I was perfectly content having intelligent conversations with him. But, ever since emotions got in the way, everything became _difficult._ " Her voice cracked, taking on a hoarser tone. "He pontificated his way into my heart, and I allowed it to happen."

She hadn't allowed herself to think about him. She tried to shut out all feelings about him, hoping that if she simply pushed them into a dark corner of her mind, they would disappear. But, underneath the bright light of the dining area, with her mother's eyes fixed on her, Amy felt every wound she had tried to conceal gape open.

She sighed deeply, her eyes flickering up to meet her mother's.

"Amelia, you cannot blame yourself for loving him. And you certainly should not expect to erase him from your life that quickly, if at all. Love is something that you cannot easily forget. You may fall in love with someone else eventually, but the memory of your first love will always remain with you. I was in a similar situation, and I did what you are trying to do now. Believe me when I say that it's the worst possible thing you can do."

She paused and in a firm voice said, "Give yourself time to heal. And healing means accepting that you loved him and still do. It does not mean forcefully pushing him out of your mind. You can revisit the good memories and analyze the bad ones to see where things went wrong. Do not place blame solely on him or yourself. A relationship takes two people whose hearts are both in it. Focus on your research and the things you need to accomplish while on sabbatical, but realize that it's perfectly acceptable to think about him. The feeling of closure occurs once you've given yourself enough time to heal."

Maria reached out to pat Amy's hand. "I know we haven't always had the best relationship, but I hope you know that you can talk to me. It helps to talk about it, you know. I bottled everything inside, and ultimately, that became my undoing."

Amy didn't know how to follow up with her mother's declaration. There was only one thing that came to mind.

"Thank you."

"No need to thank me, Amelia. I'm your mother. Giving you advice is in my job description." Maria smiled softly before lifting her now empty plate. "Are you finished with your dinner?"

"Yes. I'll help with the dishes." Amy picked up her plate and wine glass and crossed over to the sink.

Both Fowler women worked quietly, and in a matter of minutes, the task was complete. Maria turned to her daughter to bid her goodnight when she stopped in her tracks.

"Amelia, your face is contorted in concentration. You look like you're about to ask me something," she observed.

Gripping onto the kitchen counter for balance, Amy said, "I'd like to know more about my father, if that's all right with you."

Maria sat down in her seat and motioned for Amy to do the same.

Clearing her throat and shifting into a more comfortable position, Maria calmly asked, "How much would you like to know?"

"Tell me about how you two met." Amy placed her hands on either side of her face, leaning into them.

Maria smiled gently. "Let's wind back the clock, shall we?"

* * *

 _Maria Fowler glanced up from the thick tome in front of her when she heard the click of the front door swinging open. Her roommate entered the apartment with a huge grin on her face, arms full of shopping bags._

 _"I'm back!" Elizabeth Galloway announced, throwing her shopping bags on the sofa. She dramatically plopped down in the one area that wasn't covered by her purchases. Sighing contently, she rested her arms behind her head._

 _Maria chuckled, turning around from her seat at the dining room table. "I can clearly see that. Did you have a nice day?"_

 _"Of course. Retail therapy is always the best cure for living through a long and exhausting week."_

 _Maria raised an eyebrow. "How is that you had a long week? You're studying the arts. That's hardly difficult." She scoffed, shaking her head._

 _"Excuse you, Maria," Elizabeth admonished. "I, for one, believe that just because you are heavily dedicated to neuroscience and wish to become a neurosurgeon, that doesn't make you the most intelligent person on the planet. My field is challenging, too!"_

 _All Maria could do was shake her head in dismay. "Call it what you will." She raised her large textbook in the air for emphasis. "This volume, however, trumps the literature that you pour over. Honestly, you couldn't even read most of your work unless your brain was functioning properly. The brain is the most important organ of the body. And that is why I'm spending so much time studying it."_

 _Elizabeth playfully threw a pillow at Maria, which she dodged neatly. "Fighting with you over arts versus sciences is useless."_

 _"It's a moot point, Elizabeth."_

 _Rolling her eyes, Elizabeth crossed her arms over her chest. "I think you need to take a break from reading. That is all you seem to do these days, Maria."_

 _"That is not true! I'm a member of the Science Academic Bowl Team. We have our most difficult competition next week, in fact."_

 _Elizabeth sighed. "That's not what I mean. Look, every activity you do involves academics. Why don't you go watch a film, or shop, or visit a bar like everyone else?"_

 _Maria set down the book and stared at her roommate as if she had grown horns. "Given the fact that we've been living together for two years and have known one another for longer than that, surely by now you should know that my whole life revolves around academics. I don't know anything different."_

 _Elizabeth paused for a brief moment before her eyes lit up. "Okay, how about this. There's a poetry reading tonight at the coffee shop on 13_ _th_ _Street. I saw a flyer posted on one of the pillars on campus. It's from 5:00 to 7:00. See, it's perfect! Poetry readings are where all of the intelligent people are. Why don't you go with me?"_

 _Schooling her features in a way as to not offend her roommate and friend, Maria stated firmly, "No, absolutely not."_

 _"Oh, come on! I think you'll enjoy it once you arrive. Why don't you want to go?"_

 _"Elizabeth, it's a poetry reading. Enough said."_

 _Elizabeth stared at Maria, her eyes narrowing. She didn't want to have to resort to this, but desperate times called for desperate measures._

 _"If you don't go, I'll throw a party on Friday right in this very apartment. And EVERYONE will be invited, I'll make sure of it. In only a few hours, your sanctity will wreak of marijuana, alcohol, and sex. What do you think about that?"_

 _"You. Wouldn't. Dare," Maria bit out, seething._

 _Chuckling darkly, Elizabeth nodded. "Oh, but I would."_

 _Maria clutched her book protectively, grimacing at the image in her head. There was a mutual rule between the two women that stated neither could throw excessively wild parties in their shared apartment. Maria herself never had an issue, but Elizabeth was definitely more of a social butterfly. She knew people, and while she was certainly intelligent and kept up on her studies, she never failed to dapple in a good round of reckless behavior every now and then. Deep down, Maria knew Elizabeth was not bluffing. She would throw a party and wreak absolute havoc, if she needed to._

 _"Fine. I will go to this awful poetry reading for an hour and promptly leave. Once we step outside, we will never speak of it again. Do I make myself clear?"_

 _A Cheshire-cat like smile spread across Elizabeth's lips. "Crystal clear, Maria."_

 _Two hours later, Maria sat inside of the coffee shop. She faced the tiny platform that acted as a stage and scowled at her seatmate._

 _Elizabeth merely smiled and nudged her. "Don't give me that face. You know you'll probably enjoy some part of the evening."_

 _"You are sadly mistaken. Nothing could get me to enjoy this forsaken poetry reading."_

 _Maria looked around her and shuddered. People began to fill into the small space, chatting in small groups, and overall, looking happy to be there. She couldn't understand why individuals would spend their time here, when they could be at home, focusing on their studies._

 _Suddenly, the lights above the platform flashed. A woman in their thirties strolled on stage, wearing a chic black dress, black boots, and a black beret. She looked like a stereotypical theatre fanatic. Maria cringed. This was very much out of her comfort zone._

 _In a smooth, melodic voice, the lady on stage announced, "Ladies and Gentleman, I'm Lydia, the owner of Espresso Amore. Welcome to our first poetry reading. I would personally like to thank you for joining us today and listening to our special guests. We have ten people who have registered to recite their poetry, and each of them have agreed to one poem. After those ten individuals have finished, they may recite more, if they choose to. We are also going to open the floor up to ad-lib poetry. Please keep everything clean and fun. Without further ado, please give a warm welcome to our first poet, Robert Anderson."_

 _Everyone in the coffee shop snapped their fingers, which Maria took to mean that it was the 'classic' way to acknowledge one another in the poetry scene. She followed along, albeit begrudgingly._

 _A man, who appeared to be around Maria's age, strolled on stage with a small leather bound journal in his hands. She tilted her head slightly to get a better look at him. She hated to admit it, but he was quite attractive. She usually never thought that about any man she came into contact with because she had more important matters to attend to or to think about. But for some reason, she couldn't tear her eyes away from the person in front of her._

 _"Hello," he said into the standing microphone._

 _Maria tried to ignore the flutter in her abdomen. His voice was rich and strong, so unlike the squeaky voices of her male compatriots on the Science Academic Bowl Team._

 _"As Lydia said, I'm Robert. My first poem is titled, 'Wholly, Entirely, Completely.'" He flipped open his journal to the third page, took a deep breath, and began._

 _Eyes meet across a crowded room_

 _Soft smiles are exchanged, along with quiet laughter_

 _A moment of bliss, a moment of silent understanding_

 _Two souls woven together through time and space_

 _A sudden crash that brings everything to a halt_

 _A debilitating condition, one that cannot be cured_

 _And yet, it is not a heavy defeat_

 _It is the beginning of strength, of courage_

 _Because together they are whole, they are entire beings, they are complete_

 _Robert drifted off quietly, gauging the audience. For a moment, the coffee shop was silent. But, sure enough, everyone started to snap their fingers. Robert smiled, a dimple appearing on his right cheek. Nodding to the audience as a thank you, he closed his journal and stepped offstage, waving to the next person to take the stage._

 _Maria watched Robert walk to the back of the coffee shop and take a seat. He sat in silence, soaking in the poetry of the person on stage. Maria didn't even bother to look at the next poet. She kept her eyes trained on the mysterious man._

 _To anyone else, that may have seemed like an odd poem to read aloud at a coffee shop, but to Maria, she knew exactly what that poem was about. And she was impressed he even considered writing about that topic, let along crafting it in such a profoundly beautiful way._

" _You know, if you say hello, I'm sure he won't mind," Elizabeth whispered in Maria's ear._

 _Maria's cheeks immediately flushed. "I don't know what you're referring to."_

" _I may not be studying the sciences, but it doesn't take a genius to figure out that you are quite taken with him. At least make polite conversation when there's a break."_

 _Sighing, Maria nodded. "All right. If this does not go well, I blame you."_

 _After a tortuous half an hour, Lydia called for a break so the poets could rest. Robert took the opportunity to slip outside, and Maria (with obvious nudging from Elizabeth) followed him. She caught him leaning against the wall, eyes clothes, breathing in the fresh air._

 _She relaxed her shoulders from their stiff position and cleared her throat as quietly as she could._

" _Your poem was very nice."_

 _She wanted to cringe. She was an academic, for goodness sakes. She should have been able to articulate her opinion better than that._

 _Robert's eyes opened, revealing a startling shade of green. Maria had never seen eyes so green as those she was currently gazing into. One side of Robert's mouth lifted into a slightly lopsided smile, and his dimple popped out again._

" _Thank you. I'm glad that you enjoyed it. It was certainly nerve-wracking up there. This was my first performance. Poetry has always been a private hobby of mine, but a friend convinced me to sign up for tonight." He laughed, the sound silvery and light._

 _Maria blushed. He really was attractive._

" _Well, for your first performance, you were excellent. Truthfully, I didn't want to attend this event, but a friend urged me to. I wasn't expecting high quality poetry, so I was pleasantly surprised by your poem. Stephen and Jane Hawking are truly amazing people."_

 _Those green eyes lit up in surprise. "You knew the focus of my poem!"_

 _Maria smiled. "Of course. As a neuroscience student, it's only natural that I find Stephen Hawking's condition fascinating to study. I admire his work in the scientific field, even though I do not study physics myself. And as for Jane, I admire how much bravery and strength she has shown during their relationship. It's…inspiring."_

 _Robert grinned and Maria knew right then that she didn't ever want him to stop smiling. "You're in the neuroscience program at the university?"_

" _Yes." She held out her hand. "Maria Fowler."_

 _Robert returned her handshake. His grasp was gentle, but firm at the same time. "Robert Anderson, biology student with a minor in psychology."_

 _Maria laughed. "Is that how you always introduce yourself?"_

" _No, but for you, I made an exception. It's not every day that I meet an exceedingly intelligent and humble person."_

 _His words held so much sincerity that Maria almost swooned. And she never swooned for anyone._

 _Tucking her hair behind her ear, Maria glanced shyly at the floor. "Why, thank you."_

" _Maria…" Robert hesitated, which made her look up. "Sometime, when you have a moment available, would you...do me the honor of sharing a hot beverage with me? I completely understand if I'm being too forward. If so, I apologize. But, I would very much like the opportunity to speak with you on a more personal level. Your brilliant mind and kind soul have already entranced me, simply from this exchange. It would give me great pleasure if I could be in your presence again."_

 _His invitation made Maria's cheeks flush. She had never been complimented in such a way. She giggled nervously. "You don't need to be so formal, Robert. I would enjoy sharing a hot beverage with you. Do you like tea?"_

" _I love tea. One can never go wrong with English Breakfast, or any type of Darjeeling."_

 _Smiling, Maria nodded. "Wise choices. When would you like to…?"_

" _Do you have plans at the moment?"_

 _Maria shook her head. "No. I already followed my friend's order, so it seems that I am off duty. Aren't you going to stay and watch the rest of the poetry?"_

" _No. To be honest, I'm not exactly excited about ad-lib poetry." He shuddered slightly, causing Maria to chuckle. "If your friend doesn't mind, we could visit my favorite tea shop."_

 _Maria smiled, knowing how excited Elizabeth would be. "She won't mind. Let me get my jacket and I'll meet you right here in a minute."_

 _She turned on her heel to head back into the coffee shop, hiding the giddiness that was about to spread across her face._

* * *

"And that is how your father and I met," Maria finished, smiling at Amy. This smile reached her eyes, making them twinkle like she was in her twenties again.

Amy couldn't help but smile in return. "You knew right then that he was the one, didn't you?"

"Yes. I never believed in love at first sight—and I still don't—but it was the closest thing to that concept. It was just like Jane's and Stephen's first meeting. They knew that they were meant for one another, and I knew that I would love your father for the rest of my days." Her eyes glistened, but no tears had fallen.

"Do you still love him?" Amy's voice was small, quiet. She didn't want to hurt her mother by asking this, but she was desperate to know.

Maria didn't answer immediately. After what felt like an eternity to Amy, she spoke again.

"A part of me still does. Though, my love for him isn't nearly as strong as it was before. I suppose it's more of a dying ember of a once roaring fire. Time has given me perspective." She paused, considering her next words. "It was my fault in the first place. After a couple of years of marriage, I thought I wanted some distance. I cannot say for sure, but perhaps at that point, I started to fall slowly out of love with him. The actual marriage seemed overwhelming, even though we both worked and there was hardly any domesticity. However, looking back on it, I was foolish to let him go. If there is anything I regret in my life, it was acting rashly and sending him those divorce papers."

Amy sighed, leaning back in her chair. She frowned, reflecting on the story. Something didn't quite add up. Even if her mother had some concerns with her marriage, why didn't she just seek help? Amy felt a lump form in her throat. There was an explanation, but she desperately hoped it wasn't true.

"He didn't know you were pregnant with me, did he?"

Maria shook her head, the sadness evident in her eyes. "No. Had he known, he would have stayed. He would have found a way to make our marriage work. He would have done anything in his power to meet you and establish a relationship with you."

She swallowed, tears bubbling in her eyes. "Our relationship was not stable while I was struggling with my own thoughts about marriage. We didn't fight, per se, but there was an obvious chill between us. To this day, I don't understand exactly what it was, but we both felt it. As a biologist, he worked late in his lab, and as a neurosurgeon, my hours were ridiculous. We didn't see each other often, and whenever we were both home, we were exhausted. It was as if we were too tired to even try to save what we had." She stopped talking, allowing time for Amy to process the information. After a few moments of silence, she continued.

"I told him that I had been questioning our marriage and that I needed some time away from him to sort out my feelings. He acquiesced, but I knew how much it pained him that I asked him to leave for a short while."

Maria reached for Amy's hand. "We separated for a few months. During that time, I had begun to feel the early stirrings of pregnancy, so to be safe, I took the test." She gripped Amy's hand tightly in hers.

"Now, Amelia, listen to me very carefully. Do not think for a moment that I did not want you as my child. I never thought that. I had always wanted a child, but your arrival was not exactly planned. When the test came back positive, I panicked. I knew I still wasn't ready to rebuild my relationship with your father, and with a child on the way, I didn't think I could handle both. What I didn't realize, though, was that it would have been easier if he had been around. If there had been two of us to share our lives with you, everything would have been easier and in my opinion, better. But, I was young and foolish. I thought I could handle raising a child on my own. I believed I didn't need him. Ultimately, I chose having and raising you over saving any relationship I had with him. Amelia, I'm so sorry I deprived you of having a relationship with your father. It's something I won't ever forgive myself for."

Maria's eyes blinked rapidly behind her glasses as tears escaped and flowed freely down her face. Her hands flew up to hide her face in shame as she sobbed quietly.

Amy's sharp intake of breath indicated she had no idea how to handle this situation. She had never seen her mother so upset before, but remembering what worked with Sheldon when he was distraught from the Kripke incident, she did what she thought was best. She held onto her mother for dear life, soothing her cries.

"It's okay, Mother. It's okay."

Amy's own eyes prickled with tears, and as much as she wished her words were true, they weren't. It wasn't okay. She had missed out an entire life without her father—someone she believed she would have loved so much that it hurt. From what her mother told her about their first meeting, he was exactly the type of father she would have loved having.

"It's not okay, Amelia. I cannot apologize enough." Maria gently unwound Amy's arms from her thin frame. She looked at her daughter, trying to brush away her tears. "I never meant to be a horrible mother, but look what I've done? Deprived my own daughter of knowing a man who would have loved and cared for her."

Amy had had enough. Even though she couldn't quell the pain in her heart, she had to salvage this conversation.

"You are _not_ horrible mother. Why would you even think that? I will admit that your method of child-rearing was unconventional and at times, I wonder if what you did was truly the best for me. But, all of that aside, you did an excellent job raising me to become a strong and independent woman. I'm not going to pretend that I'm not hurt by the knowledge that my father doesn't know my existence, but at least I can find comfort in the fact that he _would have_ loved me. And that is enough for me. You cannot change what's already happened. The only thing we can do is to move on." With each word, Amy felt herself believe what she said.

Maria reached out to touch Amy's face. "Oh, Amelia. He would have loved you so much. Your eyes, your laughter, your love of reading and poetry, your kind heart—all of those traits you received from your father. You're definitely his daughter."

Amy placed her hand over her mother's, a sad smile on her lips. "I know."

Maria's voice was soft with her next words. "Would you like to see the other picture that I have of him? It's a special one."

"Yes, more than anything."

"Follow me and I'll show it to you."

Maria stood and headed in the direction of her bedroom. Amy trailing silently behind her, waiting in bated breath. She wondered what could be more special than their wedding photograph. When they entered the room, Maria walked slowly to her ornate wooden dresser and pulled open the bottom drawer. Her hand grasped around a medium sized picture frame and she held it up, inspecting it. Amy drew closer, taking in the sight of her parents looking so young and happy in the photograph.

They were in a park somewhere and judging by the darkness of the photograph, it was sometime during the evening. They sat side by side, leaning against an oak tree, holding hands. They managed to gaze into each other's eyes and still face the camera, which made the picture even more beautiful.

"It's gorgeous, Mother," Amy whispered, breaking the silence.

"Thank you. Do you want to know why it's so special?"

Amy nodded, feeling her pulse racing.

"Unbeknownst to your father and myself, I was pregnant at the time. I would have just been a few weeks along at that point. Amelia, we are a family in this photograph."

Amy felt the air leave her lungs. Suddenly, the room was spinning and she had to latch onto something to keep from falling over. She settled for leaning against the nearby wall, trying desperately to regain her bearings.

"You mean—I'm with my father in this photograph? I'm actually inside of you and my father is _right there_?"

"Yes. This is the only family picture we have. I'm apologize that there isn't more, but…"

"It's perfect," Amy breathed, holding her hand out to touch it. She couldn't stop staring it. It felt so surreal.

"It's yours, Amelia. Please keep it safe."

Amy tore her gaze away from the picture. "I can hang onto it, even when I leave?"

Maria's expression softened and she nodded.

Amy gently embraced her mother. "Thank you. It means more to me than you'll ever know."

Careful to extract herself out of her daughter's arms, Maria smiled, reaching up to kiss her daughter on her forehead. The action was simplistic, but something even as small as that warmed Amy's heart and reminded her that her mother loved her dearly.

"I hate to be a downer, but you look like a good night's sleep is in order. I've unloaded a lot of information on you this evening. You should rest up so that you can work tomorrow."

Rolling her eyes in a playful manner, Amy agreed. "Goodnight, Mother."

Amy turned to depart, clutching the photograph tightly in her hands. She quietly closed the door behind her and made her way into her own bedroom. With her mind on overload tonight, she knew she couldn't accomplish any more work, so she quickly dressed for bed, fed the monkeys a late night snack, and bid them goodnight.

As she settled underneath the sheets, Amy closed her eyes and dreamt of a little girl on a swing set, being pushed by a man with smiling green eyes. They laughed together under the bright sunshine and blue skies.

Amy smiled into her pillow. Maybe she never had a father around to do silly things with her, but a girl could always dream.

* * *

Maria stared out of her bedroom window for what seemed like hours. She had not felt this exhausted in a long time, but she supposed that given the emotion she had expressed tonight, the fatigue was warranted. She pressed her head against the cool glass and closed her eyes.

When her daughter had initially called and said that she would be visiting, Maria never intended to let any information about Amelia's father slip out. She had kept him a secret for so long, but somehow, even after years of practice, she couldn't quite conceal the truth. Amelia was just too much like him sometimes. And she both loved and hated it. Now here she was, debating on whether or not to change Amelia's life once again.

Opening her eyes, she reached for her cell phone on her bedside table. She dialed the number that was etched forever in her mind. The phone rang three times before someone answered.

"Hello?" a man said into the speaker, his voice rich and deep, even after all of the years that had passed.

"Robert, it's Maria," she said softly, feeling her hand tremble around her phone.

"Maria? As in, my ex-wife?" He sounded puzzled, but not angry in the slightest.

"Yes. Is this a bad time?"

"No, not at all. I was just enjoying a cup of Darjeeling."

Maria felt her lips quirk into a small smile. Some things never changed.

"I apologize for this unexpected phone call. I remember telling you that it would be best for us not to speak anymore, but I think this is an exception. I need you to listen very carefully. Can you do that for me?"

Robert didn't answer her question outright and instead said, "Is something the matter? I haven't heard from you in ages and then I get an alarming call from you." Concern colored his tone, making Maria feel guilty.

Maria sighed. "I'm all right, Robert. I need to tell you something, though. If you're currently standing, please sit down. This may take a while."

By the time Maria relayed the information to Robert, he was stunned silent. No words were exchanged by either party for nearly five minutes.

Maria broke the silence by asking, "Robert, are _you_ all right? I know that you are probably feeling overwhelmed at the moment, but I need to make sure that I do not need to contact medical personnel about your state of shock."

In the quietest and most unsure voice Maria had ever heard him use, he uttered, "I have a daughter?"

"Yes. Her name is Amelia Farrah Fowler. She is a thirty-four-year old neurobiologist at the California Institute of Technology. She plays the harp, loves medieval literature and poetry, and watches old French movies. She has your eyes, your laugh, and your smile. And more than anything in this world, she wants to know you. I kept you a secret, and I know now that it was a mistake. It wasn't until recently that I told her about you."

Maria heard her ex-husband breathe loudly through his mouth. Finally he murmured, "Am I able to see her? I just want to know that she's real. That she's my daughter."

"Yes," Maria hesitated before continuing. "That would be agreeable. But, please for the life of you, be gentle with her. She may not be ready to see you for another few weeks. Give her time to adjust."

"I promise that I will. And you're sure that I'm able to visit? I know that it's been years, Maria. And we didn't exactly leave off on the best foot."

"Robert, I'm not going to lie and say that this will be easy. I was the one who forced the divorce on you. I completely understand if you are still angry and resentful. I would be, too, if the situation had been reversed. But, I didn't call you to discuss us. This is about our daughter, the best product of our relationship. Whatever tension you and I may have between us is irrelevant when it comes to her. She deserves to know both of her parents and she deserves both of our love."

"She does. I don't even know her and I already love her."

"I know. Would you be able to visit within the next few weeks? I don't know how much longer she will be here. She's currently on sabbatical, but she plans on changing destinations at some point. She's having a journey of self-discovery, if you will."

Robert chuckled. "She sounds like my daughter."

"The resemblance is uncanny. That tangent aside, is that time frame acceptable for you?"

"Yes. I teach during the week, but I do not work on Fridays. I could visit a week from this upcoming Friday."

"Ah, you've resorted to teaching as well? And yes, that should be fine. I'll make sure Amelia is still in town for your arrival."

"Yes. I retired from my position as a biologist nearly six years ago. Now I teach graduate level biology at the University of Chicago." He paused, taking a deep breath. "I look forward to meeting her. Are you going to tell her about my visit?"

"No, it should be a surprise. I know that she would not object to seeing you. There's a part of her that's been missing and now she's found it. As I said, please be very gentle with her. She's overwhelmed right now. Take your time to get to know your daughter."

"I will. When the time comes closer, I'll call you to make sure everything is still all right."

"Wonderful." Maria swallowed around the lump in her throat. "And Robert? Thank you for giving me the best gift possible. Our daughter is a brilliant, kind woman."

"I have no doubts about that. She is a product of both of us, so thank _you,_ Maria. Have a nice evening."

He hung up the phone and Maria stared at the electronic device in her hands. Sighing, she set her cell phone down on her bed and leaned against the headboard. She sincerely hoped she had done the right thing.

* * *

 **June 14, 2015**

Penny leaned across the kitchen counter, a warm cup of coffee in her hands. With a frown, she watched Sheldon. He was in his spot on the couch, a medium sized white board in his lap, mumbling about some equation. To anyone else, he was acting perfectly normal. Well, as normal as he could ever be with all of his eccentricities.

But, Penny knew better. After years of being friends with the quirky and brilliant physicist, she could read him like a book. Just from the way he moved and the way he spoke, she could tell that he was troubled. His iron-clad façade was in place, but when he least expected it, it cracked the slightest bit to reveal all of the pain underneath.

Most people thought Penny wasn't observant, but little did they know that she noticed the small things about everyone. She had to admit that was no rocket scientist, but it didn't take a genius to figure out that Sheldon was deeply hurt by Amy's absence.

Sighing, Penny set her mug down on the island counter and turned around to put the tea kettle on. Sheldon needed a drink, and she was sure she wasn't permitted to give him alcohol at a time like this.

As she waited for the kettle to whistle, she reached for the tea box in the cabinet above her head. Smiling sadly, she thought about the many times that Amy and Sheldon had bonded over tea and scientific conversations.

Even though she had known about Amy's plans, it didn't make things any easier. Penny found herself missing the awkwardly sweet brunette, but deep down, she knew that Amy was going to be fine. Never in her life had she doubted how independent and capable Amy was. Of course, she supported Amy in her decision to leave, but she knew that in time, Amy would realize that her home was here and she would be back. It was a gut feeling—and her instincts were sharper than those around her.

In the back of Penny's mind, she was aware that revealing to Sheldon what she knew all along wouldn't be the right thing. Even though she cared about him, she had to let him figure it out on his own. He had grown quite a bit over the years, but Sheldon still had so much more maturing to do. Sometimes it was painfully obvious that he took Amy for granted, and it was something that truly bothered Penny. Amy had been mistreated her whole life by people who thought less of her; she didn't need it coming from a boyfriend, too.

When Amy had spoken to her about leaving, she had agreed with Amy that it was a correct move to test Sheldon's feelings for her, as well as her own for him. Everyone knew that Sheldon loved Amy, but how much did he really love her? Penny would be lying if she said she wasn't curious to find out herself.

The tea kettle finally whistled, startling Penny from her thoughts. She lifted it gently and poured the hot water into Sheldon's normal mug. Opening the tea box, she selected a chamomile bag from its designated spot and began to dunk into the steaming liquid. Once the tea had properly steeped, she carried it over to her friend.

"Tea, Sheldon?" she asked quietly, holding out the mug in front of him.

Sheldon glanced up from his work, a look of surprise in his blue eyes. He titled his head to the side in confusion.

"Thank you, Penny, but I didn't specifically ask for tea."

Rolling her eyes, Penny retorted, "Is there ever not a time for tea?"

"Well…"

"Are you going to drink it or not?" she demanded impatiently, tapping her foot, careful not to jostle the liquid.

Sheldon reached for the mug. "Thank you. I must ask, though. What's the occasion? You never usually make me tea. Your fiancée normally has the honor of doing such a task."

Penny sighed, sinking into her normal chair. "I'm not allowed to give you alcohol, so I figured tea was the next best thing to preface our conversation. We need to talk, Sheldon, about your... overfocusing thing."

He sipped his chamomile tea in silence before setting it down on the coaster that lay on the table near the couch.

"I have no idea what you're referring to," he replied coolly.

"Sheldon, don't act like you don't know what I'm talking about. You've been way _too_ focused on your work lately. It's driving all of us insane. All you want to do is _work, work, work._ You haven't gone to the comic book store in weeks. When the guys wanted to marathon _Star Wars_ a few days ago _,_ you holed yourself in your room for the whole weekend. You haven't played _Dungeons & Dragons _or the _Mystic Warloards of Ka'a_ in what seems like forever. All you do is go to work and come back home to do more work! Seriously, Sheldon. What gives?"

She was waiting for him to say it. He _had to_ say it. He was smart enough to know the answer she was looking for.

But, it was Sheldon, and he lived to frustrate her.

"Penny, I have been more productive in the last few months than I've ever been before. Are you saying that this is a _problem_?" he hissed, eyes narrowing into angry slits.

"Sheldon!" she growled. " _Stop._ Stop pretending that you're doing just fine. We all know you're not. The sooner you admit, the easier it will be for all of us to _help_ you!"

Immediately, Sheldon's face fell, making Penny want to kick herself. She should have been more tactful when approaching him about this topic, which was obviously still very touchy for him.

Quietly and calmly, almost _too_ calmly, Sheldon said, "I don't need help, Penny. Work is the only thing that matters to me right now. Science…science will never abandon me. Science will never hurt me. I have loved science from the beginning and that will never change. As much as I care for you, Leonard, and the rest of our friends, I just _can't_ deal with you all at the moment. Please understand." His eyes, which didn't ignite with anger anymore, were pleading her to drop the subject.

More than anything, Penny just wanted to hug him and make the pain go away. Sheldon was like a brother to her and one thing her father taught her was to be fiercely protective of family. It was difficult to see him so broken, but she had to keep reminding herself that what she was practicing was tough love. He had to come to the realization himself. But, that didn't necessarily mean she couldn't give him a hint. Or two.

"Okay," she answered softly. "I'm sorry I yelled, Sheldon. I didn't mean to."

"It's quite all right."

Something in his tone said otherwise, but she wasn't going to call him on it.

Instead, she said, "I get why work is so important, but take time for yourself, too. You need to hang out with the guys again. Tell you what? If you put your board away for dinner tonight with _everyone,_ then you can spend the next two days working and we won't bother you at all. Can you promise me that?"

He hesitated for a fraction of a second before nodding. "I'll agree to your terms."

"Good." Penny stood from her spot. "Enjoy your tea."

Sheldon was already back at it, fingers clenched around the dry erase marker.

Before making her exit out of the front door, Penny said one last thing. She turned to him, eyes settled on his face.

"She loved you. You know that, right? She loved you so much, but she deserves more. And she's out there, looking for it. Maybe she'll be back, maybe she won't. She's got to do what's best for her. But, for what it's worth, you meant the world to her."

Penny disappeared before she could catch Sheldon's expression. If she had to guess, though, he probably let his mask slip and a look of torment crossed his face. The thought twisted uncomfortably in her stomach.

 _It's for his own good,_ she thought to herself. _He needs to figure it out. It's for his own good._

She kept repeating it, _hoping_ that the more times she did, the more she would believe it. But, the one thing she knew for sure was this: brokenhearted Sheldon was possibly the worst thing she had ever witnessed.

* * *

 **A/N:**

 _Was it okay? Like I said, it's been a long time since I've written anything. Feel free to leave a review (trust me, I get really excited when I receive one). As promised, here's the playlist:  
_

 _Chapter 1: A Game of Croquet_

 _Chapter 2: Domestic Pressures_

 _Chapter 3: Forces of Attraction_


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